PLANTCARE: A PLANT CIS-ACTING REGULATORY ELEMENT DATABASE

¹ VIB Department of Genetics, University of Ghent, K.L.Ledeganckstraat 35, B-9000 GENT, Belgium

² INRA-France Associated Laboratory

PlantCARE is a relational database of plant cis-acting regulatory elements, enhancers and repressors, accessible on the web at: http://sphinx.rug.ac.be:8080/PlantCARE. Given the amount of genome sequence, strategies are necessary to discover the location and structure of the genes and to elucidate the expression of those genes and the elements regulating it. Because experimental information is lacking, in silico gene discovery through gene prediction programs is attempted, but gene modeling remained of poor quality due to the lack of descriptions of gene borders and promoters. Knowledge on cis-acting sequences regulating gene expression will become available on a large scale for plants as well as for other organisms with the genome-wide analysis of co-expressed genes. This information on promoters will, allow to allocate a potential cellular function to a gene or will offer biotechnology the possibility to control more specifically the expression of genes. Therefore the need for managing this knowledge emerged, and urged us to build an adequate database. Earlier databases, such as TFD, EPD or TRANSFAC, with the more general purpose of storing any known promoter element, have only a few cases of established plant cis-acting regulatory elements. This underrepresentation of plant data makes the systems not efficiently applicable to plant promoter sequences. We thus began to collect as much as possible information around plant promoters with their cis-acting regulatory elements and to organize them in a local relational database. As we aimed to store every known plant element and gather all the described plant promoters, we designed our database in such a way as to avoid redundancy and to have a clear view on the different sites. We stored every promoter element as we found them in the literature with the degree of confidence that we could find from their description, accordingly to the used procedures followed, as experimental procedures or homologies searches. Rombauts S. et al., 1999, Nucl. Acids Res. database issue